Depends on the purpose of the box.
For general office work, pre-built every time - they are cheaper and apart from software configuration ready to go as soon as you get them.
Agreed. And even if I custom build one (e.g. a Shuttle) I don't care for the hardware, usually go with something from the cheap end - and nothing has failed me up to date: I still have a Pentium90 with a 1GB HD running. (And if something should fail, I usually have something to replace it, and of course backups).
There really is no point in custom-built, unless there is some very special purpose, like gaming or very high reliability (where any downtime costs plenty of money). Or, of course, if you have too much time on your hands and like "playing" with hardware.